diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 173 |
1 files changed, 131 insertions, 42 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25202410e5..4cbffac000 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1971,14 +1971,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.64.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0n3yyrglzqzw0wqxl9igqvkj8qslw6yjkym3vcq0c93kkg7vk01l")))) + "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -2272,13 +2272,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.26.1") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1jx1wm47s64ywfddrg8kqzz4xpcmfjwrzbxhvlmys7pf2hzj4gbh")))) + "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -2795,13 +2795,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.34.0") + (version "3.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1ikl9y6hj2p92nrb1ydxy2410b3wrax83rfy2imaj0vgfmhsgx6g")))) + "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -3024,13 +3024,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.28.1") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1ga8yrn7j1wn9wdsvf4ws6n2987yk1yxz22v2jzaszfikhjh1sp8")))) + "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -3087,13 +3087,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.44.1") + (version "1.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0byizkq18kkyq3n604f38z4mikhi3szsrfrlz22wdq2ldq3nzkis")))) + "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -4236,6 +4236,45 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-simplifyenrichment + (package + (name "r-simplifyenrichment") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "simplifyEnrichment" version)) + (sha256 + (base32 + "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh")))) + (properties + `((upstream-name . "simplifyEnrichment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-circlize" ,r-circlize) + ("r-clue" ,r-clue) + ("r-cluster" ,r-cluster) + ("r-complexheatmap" ,r-complexheatmap) + ("r-digest" ,r-digest) + ("r-getoptlong" ,r-getoptlong) + ("r-go-db" ,r-go-db) + ("r-gosemsim" ,r-gosemsim) + ("r-matrix" ,r-matrix) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-proxyc" ,r-proxyc) + ("r-slam" ,r-slam) + ("r-tm" ,r-tm))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jokergoo/simplifyEnrichment") + (synopsis "Simplify functional enrichment results") + (description "This package provides a new clustering algorithm, binary +cut, for clustering similarity matrices of functional terms is implemented in +this package. It also provides functionalities for visualizing, summarizing +and comparing the clusterings.") + (license license:expat))) + (define-public r-trajectoryutils (package (name "r-trajectoryutils") @@ -4851,14 +4890,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.2.5") + (version "3.2.7") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1rp4sgx58g1lq5brpx07wffllhvsqq1097vrjiaksbih08338nih")))) + "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -5097,14 +5136,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.26.3") + (version "3.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "07dvg3r4kghkqhh1a8rw149hgfswmzdh9cvnam8c82006cpmi74s")))) + "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -5151,13 +5190,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "0kjsc5ghcplay4a74ffpwsf3kbp51x6rl5265gvlfchdwrawkzd2")))) + "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -5801,29 +5840,30 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.0.3") + (version "3.0.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "02ydi5iyxwrvwfjmv8pbanmzpi1r99mc4gxl17fpq2jf1d1mk6g0")))) + "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) ("r-aplot" ,r-aplot) ("r-dplyr" ,r-dplyr) + ("r-ggfun" ,r-ggfun) ("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) - ("r-rvcheck" ,r-rvcheck) ("r-scales" ,r-scales) ("r-tidyr" ,r-tidyr) ("r-tidytree" ,r-tidytree) - ("r-treeio" ,r-treeio))) + ("r-treeio" ,r-treeio) + ("r-yulab-utils" ,r-yulab-utils))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://yulab-smu.top/treedata-book/") (synopsis "R package for visualization of trees and annotation data") @@ -7398,14 +7438,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.0.4") + (version "4.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "161w9mn2plmymvzf1hkk9fwi3d9c26kbcpndyyrfcl6bg2nxr1s8")))) + "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -7421,8 +7461,8 @@ All the visualization methods are developed based on ggplot2 graphics.") ("r-plyr" ,r-plyr) ("r-qvalue" ,r-qvalue) ("r-rlang" ,r-rlang) - ("r-rvcheck" ,r-rvcheck) - ("r-tidyr" ,r-tidyr))) + ("r-tidyr" ,r-tidyr) + ("r-yulab-utils" ,r-yulab-utils))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") @@ -8850,14 +8890,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "0xgjbk35wl1vjqyq4y5c7hna8hkgmf56xjaxcph9bs2q7mbdnqwf")))) + "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -10176,14 +10216,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0kw16zf9004d1zlwsswhbcb7p77nabpd1fjagznff3zyan9fpdxf")))) + "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -10488,14 +10528,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "119qdivd7vaaqkjb0nrwidi6g26hh8znhif3g4prqn7x5pl2clvy")) + "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -10508,7 +10548,7 @@ metrics, with methods for objects produced by the @code{methylumi} and (substitute* "src/Makevars" (("all: \\$\\(SHLIB\\)") "all:") (("\\$\\(SHLIB\\): liblzma.a") "") - (("(ZLIB|LZ4)/.*") "") + (("^ (ZLIB|LZ4)/.*") "") (("CoreArray/dVLIntGDS.cpp.*") "CoreArray/dVLIntGDS.cpp") (("CoreArray/dVLIntGDS.o.*") @@ -10517,8 +10557,7 @@ metrics, with methods for objects produced by the @code{methylumi} and "PKG_LIBS = -llz4")) (substitute* "src/CoreArray/dStream.h" (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) - (string-append "include <" header ">"))) - #t)))) + (string-append "include <" header ">"))))))) (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs @@ -10711,14 +10750,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "10xgihjssnc6i03819p9gnzwfc7znanic514ar3yxzl3fhxy3yyy")))) + "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -11878,14 +11917,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "18a9mbzfmkipnv1cc9h3rhn9jxdp7nzywp0bz7hvmsaffv4p4skc")))) + "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -11904,7 +11943,6 @@ gene selection, testing relationships, and so on.") ("r-magrittr" ,r-magrittr) ("r-rbgl" ,r-rbgl) ("r-readr" ,r-readr) - ("r-rex" ,r-rex) ("r-rlang" ,r-rlang) ("r-rvest" ,r-rvest) ("r-stringr" ,r-stringr) @@ -12279,13 +12317,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.30.0") + (version "0.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0v5vxmg0a27ivgymmzfl595rcb1m3dz27r2wzbk1j97rlpwy1p4q")))) + "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -12934,14 +12972,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1avzd3fj4am9klmlx03nwq2pvgx7646yjwha1gqf0cbx5hibxy02")))) + "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -14602,6 +14640,57 @@ with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.") (license license:expat))) +(define-public r-omnipathr + (package + (name "r-omnipathr") + (version "3.0.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "OmnipathR" version)) + (sha256 + (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a")))) + (properties `((upstream-name . "OmnipathR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-curl" ,r-curl) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-igraph" ,r-igraph) + ("r-jsonlite" ,r-jsonlite) + ("r-later" ,r-later) + ("r-logger" ,r-logger) + ("r-magrittr" ,r-magrittr) + ("r-progress" ,r-progress) + ("r-purrr" ,r-purrr) + ("r-rappdirs" ,r-rappdirs) + ("r-readr" ,r-readr) + ("r-readxl" ,r-readxl) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect) + ("r-xml2" ,r-xml2) + ("r-yaml" ,r-yaml))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://saezlab.github.io/OmnipathR/") + (synopsis "OmniPath web service client and more") + (description + "This package provides a client for the OmniPath web service and many +other resources. It also includes functions to transform and pretty print +some of the downloaded data, functions to access a number of other resources. +Furthermore, OmnipathR features a close integration with the NicheNet method +for ligand activity prediction from transcriptomics data.") + (license license:expat))) + (define-public r-biscuiteer (package (name "r-biscuiteer") |